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  • vcftools site filter using bedfile

    Hi all

    I am trying to filter my vcf file in vcftools using a bed file. I am consistently getting an output vcf with 0 sites retained. Following is the command line I used:

    vcftools --gzvcf myfile.vcf.gz --recode --bed bedfile.bed --out outfile

    The log file looks like this:
    VCFtools - v0.1.6
    (C) Adam Auton 2009
    Parameters as interpreted:
    --out PsvaMvd7a
    --recode
    --gzvcf PsvaMvd7.vcf.gz
    --bed CF2_probes_mod_sorted.bed

    Scanning PsvaMvd7.vcf.gz ...
    Currently scanning CHROM: MT
    Currently scanning CHROM: 38
    Currently scanning CHROM: 35
    Currently scanning CHROM: 36
    Currently scanning CHROM: 37
    Currently scanning CHROM: 33
    Currently scanning CHROM: 32
    Currently scanning CHROM: 26.......
    Keeping 1718454 entries (out of 1718454 read)
    Done
    Filtering sites by BED file
    Kept 14 out of 14 Individuals
    Kept 0 out of 1718454 Sites
    Error:No data left for analysis!

    My bed file looks like this:

    "track name=""tiled_region"" description=""NimbleGen Tiled Regions"""
    chr1 11398149 11398377
    chr1 11398197 11398414
    chr1 11398377 11398448
    chr1 11453954 11454357
    chr1 11453999 11454327
    chr1 11456016 11456508
    chr1 11456061 11456496
    chr1 11537417 11537695
    chr1 11537488 11537637

    Appreciate any help. Thanks.
    Last edited by info_nowise; 04-19-2012, 05:58 AM. Reason: added more info

  • #2
    Are you 100% sure that's wrong?

    BEDTools can also get you the intersect between a .vcf and a .bed

    Comment


    • #3
      Yes, I am sure. However, I figured out the problem. I got rid of the letters 'chr' in the bed file, leaving only the numbers and vcftools worked!

      Comment


      • #4
        Thanks for the tip, though, swbarnes2!

        Comment

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